I looked at KTP's description of how to fool and cheat the FP+ system. With my very crude understanding of how a system like this might work, it looks like there is at least some small time gap using a FP+ and the system recognizing that you have used it. I don't know if he tried this often enough in different ways to see how long that gap exists. Maybe it's just a couple of seconds and maybe it's a few minutes or longer.
Also, at a very crude level I could see a few ways that Disney could fix this issue. One would be for the system to prohibit changing a FP+ reservation during the time window in which it could be used. And, while that would solve this issue, it would also make the system less flexible for people who want to use the system in the way for which it is intended. That would eliminate the ability to change a reservation if you find out when you get to the ride that you don't really need a FP because the standby line is so short. It would also prevent you from changing a FP+ reservation if you find that you are in a different part of the park when your return time comes up and you don't feel like running across the park to use it.
I give KTP credit for trying this out to see if it works. I would guess that Disney knows that it works this way and has been willing to live with this small loophole because of the likelihood that very few people would know about this and/or be willing to go through the steps to do it. But, once it becomes common knowledge, and more people take advantage of it, they may be forced to resolve the issue by making it less flexible.
I could compare this to the practice of not enforcing return times on FPs. If only a few people know that the windows aren't enforced, there is really no harm done. But, once it becomes common knowledge, and a significant number of people start taking advantage of it by rounding up FPs all day with the intention of using them at night, it disrupts the distribution of FPs and has to be changed.
So, while you are hailing KTP as a genius and a hero for discovering and publicizing this hole in the system, keep in mind that the end result may be a less flexible system than you would really like.
I really don't know if it is possible to design a system like this that could instantly communicate from the touch points at the attractions to the reservation system to alert it that a FP+ reservation has been used. But, if it does take a few seconds, and in that amount of time a guest could push the "done" button on his phone to change the reservation that has already been used, closing the loophole may produce a result you don't like. At some point there may have to be a tradeoff between flexibility and the security and integrity of the system.